Java

Java (or more specifically the Java virtual machine) is software that enables programs written in the Java language to operate essentially identically on multiple computer platforms, such as Microsoft Windows, Apple Mac OS X, and linux, without special adaptation to each platform. Jmol is one such program. Jmol will not operate unless Java is installed on the host computer. Since interactive molecular visualizations in Proteopedia depend upon Jmol, both Proteopedia and Jmol require Java.

Java is bundled with Mac OS X, and the Apple Software Update on Macs upgrades Java as new versions are released. Microsoft Windows does not provide Java, but it can easily be installed or updated by visiting Java.Com. The original (and still most widely used) Java is developed by Sun Microsystems (a subsidiary of Oracle Corporation), and since mid-2007, has been open-source software.

Apple adapts Java to work efficiently on OS X (citation needed). Apple Java is typically many versions behind Sun Java. For example, in March, 2011, the current Apple Java is 1.5.0_28 while Sun Java (e.g. installed on MS Windows) is 1.6.0_22.

Occasionally bugs in current java releases affect the performance of Proteopedia or Jmol. These are generally resolved in subsequent releases. In March, 2011, there are problems using copy and paste in the Jmol console on Macs.

Detecting your Java version
Jmol can be used, in any web page containing it, to report the version of Java currently installed: Click on Jmol, then on About Jmol. There are several free websites that report your java version, such as Java Tester. Java.Com also reports the java version on Windows: click on Do I Have Java?.